@TestClass(value="org.openscience.cdk.smsd.tools.ExtAtomContainerManipulatorTest") public class ExtAtomContainerManipulator extends AtomContainerManipulator
This is an extension of CDK AtomContainer. Some part of this code was taken from CDK source code and modified.
Constructor and Description |
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ExtAtomContainerManipulator() |
Modifier and Type | Method and Description |
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static void |
aromatizeMolecule(IAtomContainer mol)
This function finds rings and uses aromaticity detection code to
aromatize the molecule.
|
static IAtomContainer |
convertExplicitToImplicitHydrogens(IAtomContainer atomContainer)
Returns IAtomContainer without Hydrogen.
|
static int |
getExplicitHydrogenCount(IAtomContainer atomContainer,
IAtom atom)
Returns The number of explicit hydrogens for a given IAtom.
|
static int |
getHydrogenCount(IAtomContainer atomContainer,
IAtom atom)
The summed implicit + explicit hydrogens of the given IAtom.
|
static int |
getImplicitHydrogenCount(IAtom atom)
Returns The number of Implicit Hydrogen Count for a given IAtom.
|
static IAtomContainer |
makeDeepCopy(IAtomContainer container)
Retrurns deep copy of the molecule
|
static IMolecule |
makeDeepCopy(IMolecule container)
Retrurns deep copy of the molecule
|
static void |
percieveAtomTypesAndConfigureAtoms(IAtomContainer container)
Convenience method to perceive atom types for all
IAtom s in the
IAtomContainer , using the CDKAtomTypeMatcher . |
static IMolecule |
removeHydrogensExceptSingleAndPreserveAtomID(IAtomContainer atomContainer)
Returns IAtomContainer without Hydrogen.
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clearAtomConfigurations, convertImplicitToExplicitHydrogens, countExplicitHydrogens, countHydrogens, createAllCarbonAllSingleNonAromaticBondAtomContainer, extractSubstructure, getAllIDs, getAtomArray, getAtomArray, getAtomById, getAtomParity, getBondArray, getBondArray, getBondOrderSum, getElectronContainerArray, getElectronContainerArray, getHeavyAtoms, getIntersection, getMaximumBondOrder, getNaturalExactMass, getSingleBondEquivalentSum, getTotalCharge, getTotalExactMass, getTotalFormalCharge, getTotalHydrogenCount, getTotalNaturalAbundance, getTotalNegativeFormalCharge, getTotalPositiveFormalCharge, percieveAtomTypesAndConfigureUnsetProperties, removeHydrogens, removeHydrogensPreserveMultiplyBonded, replaceAtomByAtom, setAtomProperties, unregisterAtomListeners, unregisterElectronContainerListeners
@TestMethod(value="testMakeDeepCopy") public static IAtomContainer makeDeepCopy(IAtomContainer container)
container
- @TestMethod(value="testMakeDeepCopy") public static IMolecule makeDeepCopy(IMolecule container)
container
- @TestMethod(value="testAromatizeMolecule") public static void aromatizeMolecule(IAtomContainer mol)
mol
- input molecule@TestMethod(value="testGetExplicitHydrogenCount") public static int getExplicitHydrogenCount(IAtomContainer atomContainer, IAtom atom)
atomContainer
- atom
- @TestMethod(value="testGetImplicitHydrogenCount") public static int getImplicitHydrogenCount(IAtom atom)
atom
- @TestMethod(value="testGetHydrogenCount") public static int getHydrogenCount(IAtomContainer atomContainer, IAtom atom)
atomContainer
- atom
- @TestMethod(value="testRemoveHydrogensAndPreserveAtomID") public static IMolecule removeHydrogensExceptSingleAndPreserveAtomID(IAtomContainer atomContainer)
atomContainer
- @TestMethod(value="testConvertExplicitToImplicitHydrogens") public static IAtomContainer convertExplicitToImplicitHydrogens(IAtomContainer atomContainer)
atomContainer
- @TestMethod(value="testPercieveAtomTypesAndConfigureAtoms") public static void percieveAtomTypesAndConfigureAtoms(IAtomContainer container) throws CDKException
IAtom
s in the
IAtomContainer
, using the CDKAtomTypeMatcher
. If the
matcher finds atom matching atom type, the IAtom
will be configured
to have the same properties as the IAtomType
. If no matching atom
type is found, no configuration is performed.container
- CDKException